Substructure search procedures for macromolecular structures.

By R. Grosse-Kunstleve, Paul D. Adams. 2003

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, neutral): “D75, 861–877 Liebschner et al. Recent developments in Phenix 865 3 MAD, multiple-wavelength anomalous diffraction; MIR, multiple isomorphous replacement; SIR, single isomorphous replacement. ture Search; Grosse-Kunstleve & Adams, 2003; Bunkóczi et al., 2013), SOLVE (Terwilliger & Berendzen, 1999), ”
Using SAD data in Phaser (2011, neutral): “We have been unable to determine the substructure from these data using tools such as SHELXD and HySS.”
Phaser crystallographic software (2007, methodology): “Compilation of Phaser requires the computational crystallography toolbox (cctbx; Grosse-Kunstleve & Adams, 2003), which includes a distribution of the cmtz library (Winn et al., 2002).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “…been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement[6], heavy-atom search[18], template and pattern-based automated model-building[10, 19-21], automated macromolecular refinement[22], and iterative model-building, density…”
Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal (2016, methodology): “…differences are used to locate the atoms in the substructure (Weeks et al., 1993; Terwilliger & Berendzen, 1999; Schneider & Sheldrick, 2002; Grosse-Kunstleve & Adams, 2003) and are then used ISSN 2059-7983 along with the substructure to estimate phases for the entire structure…”
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum (2012, methodology): “In retrospect, it may have been possible to obtain the positions of the six sites by ab initio search, for example by using the HySS submodule (Grosse-Kunstleve & Adams, 2003), although careful choice of the high-resolution limit is required (truncation to 4.5 Å resolution) since a search against…”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Some algorithms combine Patterson and dual-space recycling methods [2,3].”
Introduction to phasing (2010, methodology): “However, direct methods are routinely used to find the heavy-atom substructure by programs such as Shake-and-Bake (SnB; Miller et al., 1994), SHELXD (Sheldrick, 2008), ACORN (Foadi et al., 2000) and HySS (Grosse-Kunstleve & Adams, 2003).”